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Started by upstream project "BIOFORMATS-test-repo" build number 287 originally caused by: Started by upstream project "Trigger" build number 306 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins8360995018941936643.sh + '[' zip = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45279_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:27:29,858 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:27:29,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:27:29,859 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:29,861 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:29,861 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:29,862 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:29,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:29,862 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:29,863 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:29,863 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:29,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:29,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:30,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:30,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:30,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:30,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:30,057 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:30,057 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:30,057 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:30,058 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:30,058 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:27:30,059 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:27:30,059 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-11 00:27:30,070] [main] java.version = 17.0.2 [testng] 00:27:30,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:30,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:30,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_00-27-30.log] [testng] 00:27:30,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-11 00:27:30,120] [main] testng.directory = /data [testng] [2024-12-11 00:27:30,120] [main] testng.configDirectory = /config [testng] [2024-12-11 00:27:30,128] [main] testng.multiplier = 1.0 [testng] [2024-12-11 00:27:30,129] [main] testng.in-memory = false [testng] [2024-12-11 00:27:30,129] [main] testng.allow-missing = false [testng] [2024-12-11 00:27:30,129] [main] user.language = en [testng] [2024-12-11 00:27:30,129] [main] user.country = ${user.country} [testng] [2024-12-11 00:27:30,129] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-11 00:27:30,623] [main] ---------------------------------------- [testng] [2024-12-11 00:27:30,623] [main] Total files: 22 [testng] [2024-12-11 00:27:30,623] [main] Scan time: 0.492 s (22 ms/file) [testng] [2024-12-11 00:27:30,623] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-11 00:30:33,106] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 00:30:33,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:33,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:33,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_00-30-33.log] [testng] 00:30:33,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301c4976 - End of configuration. [testng] [2024-12-11 00:30:40,855] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:30:40,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:40,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:40,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_00-30-40.log] [testng] 00:30:40,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f5dea8 - End of configuration. [testng] [2024-12-11 00:30:46,233] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:30:46,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:46,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:46,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_00-30-46.log] [testng] 00:30:46,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189bf79d - End of configuration. [testng] [2024-12-11 00:30:50,067] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 00:30:50,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:50,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:50,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_00-30-50.log] [testng] 00:30:50,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a002f1 - End of configuration. [testng] [2024-12-11 00:30:52,769] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 00:30:52,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:52,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:52,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_00-30-52.log] [testng] 00:30:52,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@524de17f - End of configuration. [testng] [2024-12-11 00:31:05,650] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:31:05,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:31:05,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:05,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_00-31-05.log] [testng] 00:31:05,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44042792 - End of configuration. [testng] [2024-12-11 00:31:09,579] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 00:31:09,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:31:09,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:09,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_00-31-09.log] [testng] 00:31:09,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51efdebe - End of configuration. [testng] [2024-12-11 00:31:22,802] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:31:22,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:31:22,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:22,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_00-31-22.log] [testng] 00:31:22,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ddc5575 - End of configuration. [testng] [2024-12-11 00:31:27,699] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:31:27,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:31:27,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:27,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_00-31-27.log] [testng] 00:31:27,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@139e39f9 - End of configuration. [testng] [2024-12-11 00:31:33,602] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:31:33,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:31:33,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:33,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_00-31-33.log] [testng] 00:31:33,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39d07b87 - End of configuration. [testng] [2024-12-11 00:31:37,571] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:31:37,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:31:37,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:37,572 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_00-31-37.log] [testng] 00:31:37,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4917ba06 - End of configuration. [testng] [2024-12-11 00:31:52,955] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:31:52,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:31:52,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:31:52,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_00-31-52.log] [testng] 00:31:52,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5af2dfdf - End of configuration. [testng] [2024-12-11 00:32:49,787] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-12-11 00:32:59,624] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-12-11 00:33:18,023] [pool-1-thread-11] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-12-11 00:33:36,103] [pool-1-thread-4] Initializing /data/imagej/scala-media.zip: [testng] [2024-12-11 00:33:42,493] [pool-1-thread-6] Initializing /data/samples/sdub.zip: [testng] [2024-12-11 00:34:05,114] [pool-1-thread-6] Initializing /data/imagej/mri-stack.zip: [testng] [2024-12-11 00:34:18,240] [pool-1-thread-2] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-11 00:34:33,592] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-12-11 00:34:38,389] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-12-11 00:35:06,015] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 12 minutes 7 seconds Finished: SUCCESS